def test_cryo_feature_overlay(self):
"""
Test behavior of CryoFeatureOverlay
"""
cnvs = miccanvas.DblMicroscopeCanvas(self.panel)
self.add_control(cnvs, wx.EXPAND, proportion=1, clear=True)
tab_mod = self.create_cryo_tab_model()
# Create a dummy stage & focus to attach to the view
stage = TMCLController(name="test_stage",
role="stage",
port="/dev/fake3",
axes=["x", "y"],
ustepsize=[1e-6, 1e-6],
rng=[[-3e-3, 3e-3], [-3e-3, 3e-3]],
refproc="Standard")
focus = TMCLController(name="test_focus",
role="focus",
port="/dev/fake3",
axes=["z"],
ustepsize=[1e-6],
rng=[[-3e-3, 3e-3]],
refproc="Standard")
tab_mod.main.stage = stage
tab_mod.main.focus = focus
fview = FeatureOverviewView("fakeview", stage=stage)
tab_mod.views.value.append(fview)
tab_mod.focussedView.value = fview
cnvs.setView(fview, tab_mod)
# Save current empty canvas
img = wx.Bitmap.ConvertToImage(cnvs._bmp_buffer)
buffer_clear = wxImage2NDImage(img)
cryofeature_overlay = wol.CryoFeatureOverlay(cnvs, tab_mod)
cnvs.add_world_overlay(cryofeature_overlay)
cryofeature_overlay.active.value = True
# Add features to the tab's features list
tab_mod.add_new_feature(0, 0)
tab_mod.add_new_feature(0.001, 0.001)
cnvs._dc_buffer.SelectObject(wx.NullBitmap) # Flush the buffer
cnvs._dc_buffer.SelectObject(cnvs._bmp_buffer)
img = wx.Bitmap.ConvertToImage(cnvs._bmp_buffer)
buffer_feature = wxImage2NDImage(img)
# Compare empty canvas with the added _features_va
assert_array_not_equal(
buffer_clear,
buffer_feature,
msg=
"Buffers are equal, which means the added _features_va didn't appear on the canvas."
)
test.gui_loop()
def test_current_pos_crosshair_overlay(self):
"""
Test behaviour of CurrentPosCrossHairOverlay
"""
cnvs = miccanvas.DblMicroscopeCanvas(self.panel)
self.add_control(cnvs, wx.EXPAND, proportion=1, clear=True)
tab_mod = self.create_simple_tab_model()
# create a dummy stage to attach to the view
stage = TMCLController(name="test",
role="test",
port="/dev/fake3",
axes=["x", "y"],
ustepsize=[1e-6, 1e-6],
rng=[[-3e-3, 3e-3], [-3e-3, 3e-3]],
refproc="Standard")
# Add a tiled area view to the tab model
logging.debug(stage.position.value)
fview = FeatureOverviewView("fakeview", stage=stage)
tab_mod.views.value.append(fview)
tab_mod.focussedView.value = fview
cnvs.setView(fview, tab_mod)
cnvs.view.show_crosshair.value = False
slol = wol.CurrentPosCrossHairOverlay(cnvs)
slol.active.value = True
cnvs.add_world_overlay(slol)
# stage start at 0,0 (cross hair at center) -> move bt 1mm, 1mm -> then back to 0,0
stage.moveAbs({'x': 1e-3, 'y': 1e-3}).result()
img = wx.Bitmap.ConvertToImage(cnvs._bmp_buffer)
buffer_ch_move = wxImage2NDImage(img)
test.gui_loop(1)
stage.moveAbs({'x': 0, 'y': 0}).result()
cnvs.update_drawing()
cnvs._dc_buffer.SelectObject(wx.NullBitmap) # Flush the buffer
cnvs._dc_buffer.SelectObject(cnvs._bmp_buffer)
img = wx.Bitmap.ConvertToImage(cnvs._bmp_buffer)
buffer_ch_center = wxImage2NDImage(img)
assert_array_not_equal(
buffer_ch_center,
buffer_ch_move,
msg=
"Buffers are equal, which means the crosshair didn't change on stage movement."
)
test.gui_loop()
def test_simple(self):
size = (32, 64)
wximage = wx.Image(*size) # black RGB
ndimage = wxImage2NDImage(wximage)
self.assertEqual(ndimage.shape[0:2], size[-1:-3:-1])
self.assertEqual(ndimage.shape[2], 3) # RGB
self.assertTrue((ndimage[0, 0] == [0, 0, 0]).all())
def test_simple(self):
size = (32, 64)
wximage = wx.EmptyImage(*size) # black RGB
ndimage = wxImage2NDImage(wximage)
self.assertEqual(ndimage.shape[0:2], size[-1:-3:-1])
self.assertEqual(ndimage.shape[2], 3) # RGB
self.assertTrue((ndimage[0,0] == [0, 0, 0]).all())
def snapshot_viewport(self, tab, filepath, exporter, anim):
""" Save a snapshot of the raw image from the focused view to the
filesystem.
:param tab: (Tab) the current tab to save the snapshot from
:param filepath: (str) full path to the destination file
:param exporter: (func) exporter to use for writing the file
:param anim: (bool) if True will show an animation
When no dialog is shown, the name of the file will follow the scheme
`date`-`time`.tiff (e.g., 20120808-154812.tiff) and it will be saved
in the user's picture directory.
"""
try:
tab_data_model = tab.tab_data_model
# Take all the streams available
streams = tab_data_model.streams.value
if not streams:
logging.info("Failed to take snapshot, no stream in tab %s",
tab.name)
return
if anim:
self.start_snapshot_animation()
# get currently focused view
view = tab_data_model.focussedView.value
if not view:
try:
view = tab_data_model.views.value[0]
except IndexError:
view = None
# let's try to get a thumbnail
if not view or view.thumbnail.value is None:
thumbnail = None
else:
# need to convert from wx.Image to ndimage
thumbnail = img.wxImage2NDImage(view.thumbnail.value,
keep_alpha=False)
# add some basic info to the image
mpp = view.mpp.value
metadata = {model.MD_POS: view.view_pos.value,
model.MD_PIXEL_SIZE: (mpp, mpp),
model.MD_DESCRIPTION: "Composited image preview"}
thumbnail = model.DataArray(thumbnail, metadata=metadata)
# for each stream seen in the viewport
raw_images = []
for s in streams:
data = s.raw # list of raw images for this stream (with metadata)
for d in data:
# add the stream name to the image
if not hasattr(d, "metadata"):
# Not a DataArray => let's try to convert it
try:
d = model.DataArray(d)
except Exception:
logging.warning("Raw data of stream %s doesn't seem to be DataArray", s.name.value)
continue
if model.MD_DESCRIPTION not in d.metadata:
d.metadata[model.MD_DESCRIPTION] = s.name.value
raw_images.append(d)
popup.show_message(self._main_frame,
"Snapshot saved in %s" % (filepath,),
timeout=3
)
# record everything to a file
exporter.export(filepath, raw_images, thumbnail)
logging.info("Snapshot saved as file '%s'.", filepath)
except Exception:
logging.exception("Failed to save snapshot")
def snapshot_viewport(self, tab, filepath, exporter, anim):
""" Save a snapshot of the raw image from the focused view to the
filesystem.
:param tab: (Tab) the current tab to save the snapshot from
:param filepath: (str) full path to the destination file
:param exporter: (func) exporter to use for writing the file
:param anim: (bool) if True will show an animation
When no dialog is shown, the name of the file will follow the scheme
`date`-`time`.tiff (e.g., 20120808-154812.tiff) and it will be saved
in the user's picture directory.
"""
try:
tab_data_model = tab.tab_data_model
# Take all the streams available
streams = tab_data_model.streams.value
if not streams:
logging.info("Failed to take snapshot, no stream in tab %s",
tab.name)
return
if anim:
self.start_snapshot_animation()
# get currently focused view
view = tab_data_model.focussedView.value
if not view:
try:
view = tab_data_model.views.value[0]
except IndexError:
view = None
# let's try to get a thumbnail
if not view or view.thumbnail.value is None:
thumbnail = None
else:
# need to convert from wx.Image to ndimage
thumbnail = img.wxImage2NDImage(view.thumbnail.value,
keep_alpha=False)
# add some basic info to the image
mpp = view.mpp.value
metadata = {
model.MD_POS: view.view_pos.value,
model.MD_PIXEL_SIZE: (mpp, mpp),
model.MD_DESCRIPTION: "Composited image preview"
}
thumbnail = model.DataArray(thumbnail, metadata=metadata)
# for each stream seen in the viewport
raw_images = []
for s in streams:
data = s.raw
if isinstance(data, tuple): # 2D tuple = tiles
data = [mergeTiles(data)]
for d in data:
# add the stream name to the image
if not hasattr(d, "metadata"):
# Not a DataArray => let's try to convert it
try:
d = model.DataArray(d)
except Exception:
logging.warning(
"Raw data of stream %s doesn't seem to be DataArray",
s.name.value)
continue
if model.MD_DESCRIPTION not in d.metadata:
d.metadata[model.MD_DESCRIPTION] = s.name.value
raw_images.append(d)
popup.show_message(self._main_frame,
"Snapshot saved in %s" % (filepath, ),
timeout=3)
# record everything to a file
exporter.export(filepath, raw_images, thumbnail)
logging.info("Snapshot saved as file '%s'.", filepath)
except Exception:
logging.exception("Failed to save snapshot")
def test_label_overlay(self):
logging.getLogger().setLevel(logging.DEBUG)
cnvs = miccanvas.DblMicroscopeCanvas(self.panel)
tab_mod = self.create_simple_tab_model()
tab_mod.tool.choices |= {TOOL_RULER, TOOL_LABEL}
view = tab_mod.focussedView.value
self.add_control(cnvs, wx.EXPAND, proportion=1, clear=True)
cnvs.setView(view, tab_mod)
gol = cnvs.gadget_overlay
test.gui_loop(0.1)
# gadget overlay with no tools
img = wx.Bitmap.ConvertToImage(cnvs._bmp_buffer)
buffer_empty = wxImage2NDImage(img)
self.assertTrue(numpy.all(buffer_empty == 0))
# Create a "big label"
p_start_pos = (-0.00055, -0.00055)
p_end_pos = (0.00055, 0.00055)
label = wol.LabelGadget(cnvs, p_start_pos, p_end_pos)
label.text = 'label1'
gol._tools.append(label)
# Create a 10 px label
v_start_pos = (500, 500)
v_end_pos = (500, 510)
offset = cnvs.get_half_buffer_size()
p_start_pos = cnvs.view_to_phys(v_start_pos, offset)
p_end_pos = cnvs.view_to_phys(v_end_pos, offset)
label = wol.LabelGadget(cnvs, p_start_pos, p_end_pos)
label.text = 'label2'
gol._tools.append(label)
# Create a 1 px label
b_start_pos = (599, 670)
b_end_pos = (599, 671)
offset = cnvs.get_half_buffer_size()
p_start_pos = cnvs.buffer_to_phys(b_start_pos, offset)
p_end_pos = cnvs.buffer_to_phys(b_end_pos, offset)
label = wol.LabelGadget(cnvs, p_start_pos, p_end_pos)
label.text = 'label3'
gol._tools.append(label)
# Add one ruler that will become the selected ruler
p_start_pos = (0, 0)
p_end_pos = (0, 0.00035)
selected_label = wol.LabelGadget(cnvs, p_start_pos, p_end_pos)
selected_label.text = 'label4'
gol._tools.append(selected_label)
# update drawing
cnvs.update_drawing()
test.gui_loop(0.1)
# ruler overlay with 4 labels
cnvs._dc_buffer.SelectObject(wx.NullBitmap) # Flush the buffer
cnvs._dc_buffer.SelectObject(cnvs._bmp_buffer)
img = wx.Bitmap.ConvertToImage(cnvs._bmp_buffer)
new_buffer = wxImage2NDImage(img)
assert_array_not_equal(
buffer_empty,
new_buffer,
msg="Buffers are equal, which means that the labels were not drawn"
)
# make the last label the selected one (highlighted)
gol._selected_tool = selected_label
gol._selected_tool.text = 'selected_label'
cnvs.update_drawing()
test.gui_loop(0.1)
# ruler overlay with 4 labels, 1 of them is selected (highlighted)
cnvs._dc_buffer.SelectObject(wx.NullBitmap) # Flush the buffer
cnvs._dc_buffer.SelectObject(cnvs._bmp_buffer)
img = wx.ImageFromBitmap(cnvs._bmp_buffer)
sel_buffer = wxImage2NDImage(img)
assert_array_not_equal(
new_buffer,
sel_buffer,
msg="Buffers are equal, which means that the labels were not drawn"
)
# Create a ruler
v_start_pos = (500, 500)
v_end_pos = (500, 510)
offset = cnvs.get_half_buffer_size()
p_start_pos = cnvs.view_to_phys(v_start_pos, offset)
p_end_pos = cnvs.view_to_phys(v_end_pos, offset)
ruler = wol.RulerGadget(cnvs, p_start_pos, p_end_pos)
gol._tools.append(ruler)
# Update drawing
cnvs.update_drawing()
test.gui_loop(0.1)
# Gadget overlay with 4 rulers and 1 label
# Ruler overlay with 4 rulers
cnvs._dc_buffer.SelectObject(wx.NullBitmap) # Flush the buffer
cnvs._dc_buffer.SelectObject(cnvs._bmp_buffer)
img = wx.Bitmap.ConvertToImage(cnvs._bmp_buffer)
rul_buffer = wxImage2NDImage(img)
assert_array_not_equal(
sel_buffer,
rul_buffer,
msg="Buffers are equal, which means that the ruler was not drawn")
